Running with .net 2.0 and .net 1.1 simultaneously

Make sure your run aspnet_regiis -r from the appropriate .net framework dir

For other than ASP.NET issues refer to the registry setting fix of MS OnlyUseLatestCLR = 0 or 1

You can activate this switch either by setting a registry key or by setting an environment variable:
Activate/Deactivate the Switch Using a Registry Key
Turn on the switch using the following registry setting:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\.NETFramework\OnlyUseLatestCLR=dword:00000001
Turn off the switch using the followikng registry setting:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\.NETFramework\OnlyUseLatestCLR=dword:00000000
Activate/Deactivate the Switch Using an Environment Variable
Activate the switch using the following variable set to “1”, as follows: COMPLUS_OnlyUseLatestCLR=1
Deactivate the switch using the following variable set to “0”, as follows: COMPLUS_OnlyUseLatestCLR=0
You can find a sample using the registry to activate/deactivate the switch posted on GotDotNet,
at the following URL: http://www.gotdotnet.com/Community/UserSamples/Details.aspx?
SampleGuid=4caff66c-df51-40ab-bd88-090d34e77520

and reboot

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